3rd-7th June 2024

To foster international participation, this course will be held online

General Topic: Evolution of transposable elements and their bioinformatic analysis

Transposable elements (TEs) are selfish genetic elements which exist in virtually all eukaryotic genomes. Because TEs contain regulatory or coding sequences for their own ‘survival’ and often occur in large numbers within a genome, they can have strong effects on the transcription or the epigenetic regulation of nearby genes and significantly promote structural variation or genome size expansion. The analysis of TEs is thus important for many studies in genomics and evolutionary biology. However, TEs are rapidly evolving due to arms races with their host genomes and thus often remain undetected in newly sequenced genomes. One may argue that in-depth annotation of TEs is currently one of the biggest bottlenecks in genomics research of non-model organisms. Furthermore, their repeatedness makes them challenging to study using conventional bioinformatic tools.  Indeed, computational TE analyses require knowledge of TE biology as well as awareness of the pitfalls  to overcome in diverse applications (genome annotation, TE classification, insertions polymorphism, transcriptomics) . The present course aims to address these challenges by teaching TE biology, computational analyses of TEs in genome assemblies and raw read data (building de-novo TE library, TE quantification, Insertion polymorphism) as well as transcriptomics (differential expression of TE families), and the manual analyses of TEs (consensus curation, classification).

At the end of this course, attendants should be able to conduct computational analyses of TEs, interpret the results in the light of TE biology, and improve TE annotations through manual curation. The participants will also have the opportunity to discuss their own projects and receive guidance regarding TE analysis. To achieve this, each day will be composed of lectures on TE biology and practical sessions covering diverse bioinformatic analyses. Each day will be concluded with an informal and facultative open discussion regarding the themes covered in the class. The last day will include a dedicated session where attendees will be able to explore strategies related to their own project and  further refine their  skills in computational and manual analyses of TEs.

The course is aimed at biologists at any career stage who are new to TE analyses and/or de-novo annotation of the repetitive fraction of non-model genomes.

Attendants will need to use the command line (UNIX/Shell on Linux and MacOS, Cygwin on Windows) and a sequence alignment program (e.g., BioEdit, AliView) on their computer. Basic knowledge of these will be helpful but is not required. Attendants are encouraged to bring their own genome assembly raw read and/or transcriptomic data, though this will not be required to take advantage of the training.